Mohsen Mahdawi, an organizer of the pro-Palestinian movement at Columbia University, was freed from federal custody on Wednesday, more than two weeks after immigration officials detained him and sought to rescind his green card as part of a widening crackdown against student protesters.

In releasing Mr. Mahdawi on bail, Judge Geoffrey W. Crawford of Federal District Court in Vermont drew parallels between the current political climate and McCarthyism.

“This is not the first time that the nation has seen chilling action by the government intended to shut down debate,” Judge Crawford said.

The release of Mr. Mahdawi, a permanent legal resident, is a defeat for the Trump administration, though it does not mean the end of the federal government’s action against him. His immigration case will continue, but he will be able to fight it from outside a detention facility.

Mr. Mahdawi struck a defiant tone after his release.

“I am saying it clear and loud, to President Trump and his cabinet: I am not afraid of you,” he said.

The secretary of state, Marco Rubio, has argued that protesters like Mr. Mahdawi have spread antisemitism, while demonstrators say criticism of Israel’s actions in Gaza is not antisemitic.

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